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Bioconductor - ideal (development version)

ideal

This is the development version of ideal; for the stable release version, see ideal.

Interactive Differential Expression AnaLysis

Bioconductor version: Development (3.22)

This package provides functions for an Interactive Differential Expression AnaLysis of RNA-sequencing datasets, to extract quickly and effectively information downstream the step of differential expression. A Shiny application encapsulates the whole package. Support for reproducibility of the whole analysis is provided by means of a template report which gets automatically compiled and can be stored/shared.

Author: Federico Marini [aut, cre] ORCID: 0000-0003-3252-7758

Maintainer: Federico Marini <marinif at uni-mainz.de>

Citation (from within R, enter citation("ideal")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("ideal")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ideal")
Details biocViews DifferentialExpression, GUI, GeneExpression, GeneSetEnrichment, ImmunoOncology, QualityControl, RNASeq, ReportWriting, Sequencing, ShinyApps, Software, Visualization Version 2.3.0 In Bioconductor since BioC 3.5 (R-3.4) (8 years) License MIT + file LICENSE Depends topGO Imports DESeq2, SummarizedExperiment, mosdef(>= 1.1.0), GenomicRanges, IRanges, S4Vectors, ggplot2 (>= 2.0.0), heatmaply, plotly, pheatmap, IHW, gplots, UpSetR, goseq, stringr, dplyr, limma, GOstats, GO.db, AnnotationDbi, shiny (>= 0.12.0), shinydashboard, shinyBS, DT, rentrez, rintrojs, rlang, ggrepel, knitr, rmarkdown, shinyAce, BiocParallel, grDevices, graphics, base64enc, methods, utils, stats System Requirements URL https://github.com/federicomarini/ideal https://federicomarini.github.io/ideal/ Bug Reports https://github.com/federicomarini/ideal/issues See More Package Archives

Follow Installation instructions to use this package in your R session.

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